3ZFS

Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	FrhB/FdhB-like	8045905	3002602	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Fer4_21_1	e3zfsB2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
B	Oxidored_q6	e3zfsB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
C	FrhB_FdhB_C	e3zfsC1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: FrhB_FdhB_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
B	PF13187	4Fe-4S dicluster domain (Fer4_9)	4Fe-4S dicluster domain	-	Family
B	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
C	PF04422	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term (FrhB_FdhB_N)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term	-	Family
C	PF04432	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus (FrhB_FdhB_C)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum fo ...	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	F420-REDUCING HYDROGENASE, SUBUNIT ALPHA	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding ion binding nickel cation binding metal ion binding oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding ion binding nickel cation binding metal ion binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding	-	-
B	F420-REDUCING HYDROGENASE, SUBUNIT GAMMA	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding	-	-
C	F420-REDUCING HYDROGENASE, SUBUNIT BETA	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity coenzyme F420 hydrogenase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding flavin adenine dinucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017682	Coenzyme F420 hydrogenase, subunit alpha	Family
A	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
A	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
A	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B	IPR017681	Coenzyme F420 hydrogenase, subunit gamma	Family
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
B	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
C	IPR045220	Oxidoreductase FRHB/FDHB/HCAR-like	Family
C	IPR007516	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal	Domain
C	IPR017679	Coenzyme F420 hydrogenase subunit beta, archaea	Family
C	IPR007525	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.